High accuracy of relative defect locations for repeater analysis

Methods and systems for transforming positions of defects detected on a wafer are provided. One method includes aligning output of an inspection subsystem for a first frame in a first swath in a first die in a first instance of a multi-die reticle printed on the wafer to the output for corresponding frames, swaths, and dies in other reticle instances printed on the wafer. The method also includes determining different swath coordinate offsets for each of the frames, respectively, in the other reticle instances based on the swath coordinates of the output for the frames and the corresponding frames aligned thereto and applying one of the different swath coordinate offsets to the swath coordinates reported for the defects based on the other reticle instances in which they are detected thereby transforming the swath coordinates for the defects from swath coordinates in the other reticle instances to the first reticle instance.